We are developing tools for protein structure comparison based on interatomic distances. Defining the best frame of reference for describing change is the heart of the problem. Interatomic distances have the quality of being orientation independent which facilitates analysis of an ensemble of structures. Our first data set is composed of ligated HIV protease structures. We aim to understand rules which govern structural fluctuations observed among the set. The resources of the Computer Graphics Laboratory are utilized to view different models of the HIV protease for comparison.